If you work across many computers (and even otherwise!), it's a good idea to keep a copy of your setup on the cloud, preferably in a git repository, and clone it on another machine when you need.
Thus, you should keep the .vim directory along with your .vimrc version-controlled.
But when you have plugins installed inside .vim/bundle (if you use pathogen), or inside .vim/pack (if you use Vim 8's packages), keeping a copy where you want to be able to update the plugins (individual git repositories), as well as your vim-configuration as a whole, requires you to use git submodules.
Initialize a git repository inside your .vim directory, add everything (including the vimrc), commit and push to a GitHub/BitBucket/GitLab repository:
cd ~/.vim